From 91f55717abd05a5808eb6b3a0b397bee4e8edd09 Mon Sep 17 00:00:00 2001 From: Ludovic Courtès Date: Sun, 21 Jul 2019 23:19:58 +0200 Subject: gnu: Explicitly refer to 'guile-json-1' when needed. * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change 'guile-json' to 'guile-json-1'. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (artanis)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (jupyter-guile-kernel)[inputs]: Likewise. * gnu/packages/guile-xyz.scm (guile-mastodon)[inputs]: Likewise. * gnu/packages/mail.scm (mumi)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise. * gnu/packages/package-management.scm (guix-daemon)[inputs]: Likewise. * gnu/packages/web.scm (hpcguix-web)[inputs]: Likewise. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5412440fb1..89f1ac36ea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8427,7 +8427,7 @@ library implementing most of the pipeline's features.") `(("r-minimal" ,r-minimal) ("r-rcas" ,r-rcas) ("guile-next" ,guile-2.2) - ("guile-json" ,guile-json) + ("guile-json" ,guile-json-1) ("guile-redis" ,guile-redis))) (native-inputs `(("pkg-config" ,pkg-config))) -- cgit v1.2.3 From d9340de9031211c220b5b710e64af29e066f26f2 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Tue, 25 Jun 2019 20:48:54 +0200 Subject: gnu: khmer: Make gzip timestamps writable. * gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase to make gzip timestamps writable. Signed-off-by: Efraim Flashner --- gnu/packages/bioinformatics.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89f1ac36ea..bcec9cd279 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018 Mădălin Ionel Patrașcu ;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2019 Brian Leung ;;; ;;; This file is part of GNU Guix. ;;; @@ -4206,8 +4207,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (modify-phases %standard-phases (add-after 'unpack 'set-cc (lambda _ (setenv "CC" "gcc") #t)) - ;; FIXME: This fails with "permission denied". - (delete 'reset-gzip-timestamps)))) + + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure .gz files are writable so that the + ;; 'reset-gzip-timestamps' phase can do its work. + (let ((out (assoc-ref outputs "out"))) + (for-each make-file-writable + (find-files out "\\.gz$")) + #t)))))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) -- cgit v1.2.3